Please note that running task end_to_end, phamer, phagcn, phatyp, and cherry, will automatically run phavip. The output files are the same but the supplementary files will be dumped into the corresponding task.

Input

• Contig sequences in FASTA format
• Optionally own predicted protein sequences can be given (by default the tool will use prodigal and diamond blastp for the prediction)

Output

A tabular dataset with the following columns:

• Accession: the accession or the name of the input contigs.
• Length: the length of input contigs.
• Protein_num: total number of predicted proteins.
• Annotated_num: number of proteins that have significant alignments.
• Annotation_rate: percentage of proteins that have annotations.

In addition the gene annotation itself can be produced:

• Genome: the accession or the name of the input contigs.
• ORF: the ID of the translated protein.
• Start: start position on the genome.
• End: end position on the genome.
• Strand: forward (1) or backward(-1).
• GC: GC content.
• Annotation: the annotation of the proteins.

Please note that there are two kinds of hypothetical protein:

• hypothetical protein (no hit): a protein has no alignment results to the reference database.
• hypothetical protein (no hit): a protein has alignment results but the annotation is "hypothetical protein"